[gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27
ljggmx at yahoo.com.sg
Tue Sep 6 05:03:16 CEST 2011
Why not use CHARMM36 FF? It is available in gromacs user contribution website.
If I remember correctly, charmm27 cannot yield correct area/lipid, you need to
apply surface tension.
From: Jackson Chief <jchiefelk at gmail.com>
To: gmx-users at gromacs.org
Sent: Monday, 5 September 2011 21:20:48
Subject: [gmx-users] Error when performing grompp on lipid bilayer modeled with
I want to make a model of a GPCR inserted into lipid bilayer. I obtained the
structure file for a solvated POPC bilayer from the CHARMM-GUI site. I used
CHARMM27 force field to model the bilayer and pdb2gmx had no problem generating
the *.gro, *.top, and posre.itp files. When I perform grompp I receive the
following warning and error;
"WARNING 1 [file ffnonbonded.itp, line 130]:
Overriding atomtype HOL"
"ERROR 1 [file bilayer.top, line 271489]:
No default U-B types"
I though that the issue with creating Urey-Bradley interactions using pdb2gmx
had been corrected in Gromacs-4.5.4. Please give me some advice on how to
Jackson Chief Elk
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